Leica Microsystems, in collaboration with Bitesize Bio, presents an in-depth technical eBook exploring how modern ultramicrotomy is evolving to support high-resolution electron microscopy, 3D imaging, correlative microscopy, polymer analysis, and AI-assisted research.
For decades, ultramicrotomy has been an essential technique for preparing ultra-thin samples for transmission electron microscopy (TEM) and scanning electron microscopy (SEM). However, as microscopy workflows become more complex, researchers increasingly require consistent section thickness, precise targeting, reduced sample loss, and reproducible results.
This eBook explores how automation, fluorescence navigation, 3D micro-CT integration, and AI-powered image analysis are transforming traditional sectioning into a more precise and standardised workflow.
The guide also highlights the Leica UC Enuity ultramicrotome and its capabilities for improving sectioning quality, automating sample alignment, and supporting advanced microscopy applications.
What you will learn
- How to achieve consistent, high-quality ultrathin sections for electron microscopy.
- How to preserve fluorescence signals during resin embedding.
- How to use 3D micro-CT data to identify and target structures inside resin blocks.
- How fluorescence-guided trimming can reduce sample loss.
- How automated knife and sample alignment improves sectioning reproducibility.
- How to select appropriate sectioning techniques for different polymer materials.
- How room-temperature and cryogenic ultramicrotomy differ.
- How Volume EM and AI-assisted segmentation support 3D biological reconstruction.
- How automated workflows can reduce operator variability and improve laboratory productivity.
Inside the eBook: Eight technical chapters
Chapter 1: High Quality Sectioning in Ultramicrotomy
Explores the importance of uniform section thickness, clean cutting edges, and stable section ribbons. It explains how variations in thickness can compromise 3D reconstruction and quantitative measurements.
The chapter discusses interference colours as a practical indicator of section thickness, including the typical 50–100 nm range used for TEM.
Chapter 2: In-Resin Fluorescence Protocols for Ultramicrotomy
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Explains how fluorescence signals can be preserved during sample preparation using high-pressure freezing, freeze substitution, and acrylic resins such as Lowicryl HM20 and LR White.
It demonstrates how fluorescence can help researchers locate specific labelled structures within resin-embedded samples and support correlative light and electron microscopy (CLEM).
Chapter 3: Automatic Trimming of a Target Plane Using 3D Micro-CT Data
How to Save Time and Samples by Automated Ultramicrotomy | Learn & Share | Leica Microsystems
Explores how 3D micro-CT imaging reveals structures hidden inside resin blocks before sectioning begins.
The chapter demonstrates how Leica UC Enuity’s 3D Trim module uses volumetric imaging data to define target planes and calculate the necessary sample orientation. A C. elegans example demonstrates trimming precision below 10 µm.
Chapter 4: How to Automatically Obtain Fluorescent Cells of Interest in a Block-Face
Explains fluorescence-guided block-face imaging and automated trimming to locate labelled cells without relying on repeated exploratory cuts.
It highlights the use of preserved fluorescence signals, motorised trimming routines, and integrated imaging to improve targeting efficiency and reduce sample waste.
Chapter 5: Automatic Alignment of Sample and Knife for High Sectioning Quality
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Examines how incorrect alignment between the knife and sample can cause folds, chatter, compression, and damaged section ribbons.
The chapter explains camera-guided alignment, motorised adjustments, and automated positioning to improve section quality and reduce operator-dependent errors.
Chapter 6: Mastering Polymer Sectioning – An Interview with Helmut Gnaegi
Provides expert insights from Helmut Gnaegi of Diatome on the challenges of polymer sectioning.
Topics include knife geometry, sample mounting, room-temperature versus cryogenic sectioning, material deformation, and techniques for preserving delicate polymer structures.
Chapter 7: Ultramicrotome Sectioning of Polymers for TEM Analysis
Ultramicrotome Sectioning of Polymers for TEM Analysis | Learn & Share | Leica Microsystems
Demonstrates practical polymer sectioning workflows using the Leica UC Enuity.
The chapter examines rigid polymers, including poly(styrene)-b-poly(methyl methacrylate), sectioned at room temperature, and softer polymers, including poly(styrene)-b-poly(isoprene), sectioned under cryogenic conditions.
It explains how selecting the correct temperature and embedding method helps preserve nanoscale structures for TEM analysis.
Chapter 8: Volume EM and AI Image Analysis
Volume EM and AI Image Analysis | Learn & Share | Leica Microsystems
Explores the combination of automated serial sectioning and AI-assisted image segmentation.
Using Leica’s AIVIA software, researchers can identify and reconstruct organelles such as nuclei, flagella, hydrogenosomes, lysosomes, and vacuoles.
The chapter demonstrates how deep-learning segmentation, manual refinement, and quantitative analysis can transform large electron microscopy datasets into detailed 3D biological models.
Key technologies and applications covered
| Technology | Primary application |
|---|---|
| Ultramicrotomy | High-quality ultrathin section preparation |
| In-resin fluorescence | Targeted cellular imaging |
| 3D micro-CT | Internal structure identification |
| Automated trimming | Reduced sample loss |
| Camera-guided alignment | Reproducible sectioning |
| Cryo-ultramicrotomy | Soft polymer sectioning |
| Volume EM | Three-dimensional reconstruction |
| AI segmentation | Automated image analysis |
Who should read this eBook?
This technical resource is particularly relevant for:
- Electron microscopy researchers and specialists.
- Life science and cell biology researchers.
- Materials science and polymer researchers.
- TEM and SEM laboratory professionals.
- CLEM and Volume EM specialists.
- Microscopy core facility managers.
- Research scientists working with resin-embedded samples.
- Laboratories exploring automated microscopy workflows.
Conclusion
Modern microscopy demands more than the ability to produce thin sections. Researchers need reliable sample preparation, precise targeting, consistent alignment, and scalable workflows capable of supporting increasingly complex imaging applications.
This eBook demonstrates how these requirements can be addressed through the integration of automation, fluorescence imaging, micro-CT targeting, advanced polymer sectioning, and AI-powered analysis.
By connecting sample preparation with downstream imaging and interpretation, Leica Microsystems illustrates how ultramicrotomy is evolving from a highly specialised manual technique into a more reproducible and integrated research workflow.
Download Precision Ultramicrotomy: Application-Driven Innovations for Sectioning Resin-Embedded Samples to explore practical techniques, expert insights, and emerging technologies shaping the future of electron microscopy.
